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S H Chou

Publications and source records attributed to S H Chou.

At least 55 records · Page 3Linked to original sources
PubMed1992

Base pairing geometry in GA mismatches depends entirely on the neighboring sequence.

We have synthesized nine self-complementary DNA oligomers containing different flanking sequences adjacent to a pair of contiguous GA mismatches, and have used high resolution nuclear magnetic resonance (n.m.r.) to investigate the GpA phosphodiester backbone conformation and mismatch pairing schemes in these duplexes. We found dramatic effects of the flanking base pair on the hydrogen bonding and backbone conformation, which appear to be coupled. Thus the Ganti-Aanti base pairing scheme in a NAGATN sequence switches to a more stable sheared GA base pairing scheme in a NCGAGN or NTGAAN context, while no duplex is formed (or only GA bulges occur) when NAGATN is changed to NGGACN. Furthermore, the more stable sheared GA pairing in NPyGAPuN sequences is associated with a BII rather than BI backbone conformation for the phosphodiester between the adjacent mismatched GA pairs. The overall stability of these adjacent GA mismatches as measured by imino proton n.m.r. studies is Py-GA-Pu > A-GA-T > G-GA-C.

Base Composition↗
PubMed1992

Solution structure of [d(GCGTATACGC)]2.

The solution structure of the alternating pyrimidine-purine DNA duplex [d(GCGTATACGC)]2 has been determined using two-dimensional nuclear magnetic resonance techniques and distance geometry methods. Backbone distance constraints derived from experimental nuclear Overhauser enhancement and J-coupling torsion angle constraints were required to adequately define the conformation of the inter-residue backbone linkages and to avoid underwinding of the duplex. The distance geometry structures were further refined by back-calculation of the two-dimensional nuclear Overhauser enhancement spectra to correct spin-diffusion distance errors. Fifteen final structures for [d(GCGTATACGC)]2 were generated from the refined experimental distance bounds. These structures all exhibit fully wound B-form geometry with small penalty values (< 1.5 A) against the distance bounds and small pair-wise root-mean-square deviation values (typically 0.6 A to 1.5 A). The final structures exhibit positive base-pair inclination with respect to the helix axis, a marked alternation in rise and twist, and are shorter and wider than classical fiber B-form DNA. The purines were found to adopt a sugar pucker close to the C-2'-endo conformation while pyrimidine sugars exhibited significantly lower pseudorotation phase angles in the C-1'-exo to C-2'-endo range. The minor groove cross-strand steric clashes at pyrimidine-purine steps that would exist in pure B-DNA are attenuated by an increased rise at these steps (and an increased roll angle at TpA steps). Concomitantly the backbone torsion angles of the pyrimidine moieties have larger gamma values, larger epsilon values, and smaller zeta values than the purines. The structures generated by distance geometry methods were also compared with those obtained from restrained molecular dynamics with empirical force-field potentials. The results indicate that the nuclear magnetic resonance/distance geometry approach alone is capable of elucidating most of the salient structural features of double-stranded helical nucleic acids in solution without resorting to empirical energy potentials and without using any structural assumptions from crystallographic data.

Base Sequence↗
PubMed1992

Solution structure of [d(ATGAGCGAATA)]2. Adjacent G:A mismatches stabilized by cross-strand base-stacking and BII phosphate groups.

The solution structure of a rather unusual B-form duplex [d(ATGAGCGAATA)]2 has been determined using two-dimensional nuclear magnetic resonance (2D-NMR) and distance geometry methods. This sequence forms a stable ten base-pair B-form duplex with 3' overhangs and two pairs of adjacent G:A mismatches paired via a sheared hydrogen-bonding scheme. All non-exchangeable protons, including the stereo-specific H-5'S/H-5'R of the 3G and 7G residues, were assigned by 2D-NMR. The phosphorus spectrum was assigned using heteronuclear correlation with H-3' and H-4' reasonances. The complete assignments reveal several unusual nuclear Overhauser enhancements (NOEs) and unusual chemical shifts for the neighboring G:A mismatch pairs and their adjacent nucleotides. Inter-proton distances were derived from time-dependent NOEs and used to generate initial structures, which were further refined by iterative back-calculation of the two-dimensional nuclear Overhauser enhancement spectra; 22 final structures were calculated from the refined distance bounds. All these final structures exhibit fully wound helical structures with small penalty values against the refined distance bounds and small pair-wise root-mean-square deviation values (typically 0.5 A to 0.9 A). The two helical strands exchange base stacking at both of the two G:A mismatch sites, resulting in base stacking down each side rather than down each strand of the twisted duplex. Very large twist angles (77 degrees) were found at the G:A mismatch steps. All the final structures were found to have BII phosphate conformations at the adjacent G:A mismatch sites, consistent with observed downfield 31P chemical shifts and Monte-Carlo conformational search results. Our results support the hypothesis that 31P chemical shifts are related to backbone torsion angles. These BII phosphate conformations in the adjacent G:A mismatch step suggest that hydrogen bonding of the G:A pair G-NH2 to a nearby phosphate oxygen atom is unlikely. The unusual structure of the duplex may be stabilized by strong interstrand base stacking as well as intrastrand stacking, as indicated by excellent base overlap within the mismatch stacks.

Base Composition↗
PubMed1992

Errors in RNA NOESY distance measurements in chimeric and hybrid duplexes: differences in RNA and DNA proton relaxation.

Nuclear magnetic resonance experiments reveal that the base H8/H6 protons of oligoribonucleotides (RNA) have T1 relaxation times that are distinctly longer than those of oligodeoxyribonucleotides (DNA). Similarly, the T1 values for the RNA H1' protons are approximately twice those of the corresponding DNA H1' protons. These relaxation differences persist in single duplexes containing covalently linked RNA and DNA segments and cause serious overestimation of distances involving RNA protons in typical NOESY spectra collected with a duty cycle of 2-3 s. NMR and circular dichroism experiments indicate that the segments of RNA maintain their A-form geometry even in the interior of DNA-RNA-DNA chimeric duplexes, suggesting that the relaxation times are correlated with the type of helix topology. The difference in local proton density is the major cause of the longer nonselective T1s of RNA compared to DNA, although small differences in internal motion cannot be completely ruled out. Fortunately, any internal motion differences that might exist are shown to be too small to affect cross-relaxation rates, and therefore reliable distance data can be obtained from time-dependent NOESY data sets provided an adequately long relaxation delay is used. In hybrid or chimeric RNA-DNA duplexes, if the longer RNA relaxation times are not taken into account in the recycle delay of NOESY pulse sequences, serious errors in measuring RNA proton distances are introduced.

Base Sequence↗
PubMed1992

Familial spontaneous pneumothorax-report of seven cases in two families.

Spontaneous pneumothorax usually occurs sporadically in healthy young adults, who tend to be tall and thin. The usual cause is rupture of small subpleural bullae found in the apex of the upper lobe. Familial spontaneous pneumothorax is a rare condition. With a review of the English literature from 1921 to 1991, only 59 families with 135 cases have been reported. A genetic background has been suggested, but the actual mode of inheritance is still unknown. Relationships between the HLA haplotype A2B40, the alpha1-antitrypsin phenotype and the occurrence of spontaneous pneumothorax have been proposed, but are still controversial. We present 7 patients in 2 families with 13 episodes of spontaneous pneumothorax. Neither congenital defect, alpha1-antitrypsin deficiency nor the described A2B40 HLA haplotype could be found in our patients. We propose that there are no such factors existed in these patients. Further study is required to determine if any genetic marker is linked to familial spontaneous pneumothorax.

Adult↗
PubMed1991

A modified Arg-Asp-Val (RDV) peptide derived during the synthesis of Arg-Glu-Asp-Val (REDV), a tetrapeptide derived from an alternatively spliced site in fibronectin, inhibits the binding of fibrinogen, fibronectin, von Willebrand factor and vitronectin to activated platelets.

Characterization of a side-product obtained during the synthesis of Arg-Glu-Asp-Val (REDV) with inhibitory activity in thrombin-activated platelet aggregation was carried out. The semipreparative column fractionation of REDV peptide was rechromatographed on an analytical HPLC column and revealed two peaks which were re-tested for inhibitory activity. Using amino acid analysis with sequencing and fast atom bombardment mass spectrometry (FABMS), the first peak was determined to be REDV with molecular mass of 517 Da, and the second peak was determined to be a modified RDV with a mass of 608 Da. The modified RDV peptide inhibited thrombin-induced platelet aggregation with an IC50 of 200 microM, and complete inhibition occurred at 600 microM. However, the REDV peptide did not inhibit platelet aggregation up to 1 mM concentration. The modified RDV peptide eluted platelet glycoprotein IIb-IIIa complex that had been bound to GRGDSP-agarose. These studies show that the modified RDV peptide interacts with the platelet glycoprotein IIb-IIIa complex. Based on the collision-induced dissociation (CID) mass spectral data analysis, the modified RDV peptide has been characterized to contain an N-terminus blocking group on the Arg residue. The origin of this blocking group is presumed to have originated from decomposition products of the phenylacetamidomethyl (PAM) resin used in the solid-phase synthesis of the target peptide Arg-Glu-Asp-Val.

Amino Acid Sequence↗
PubMed1991

Hepsin, a cell membrane-associated protease. Characterization, tissue distribution, and gene localization.

Hepsin, a putative membrane-bound serine protease, was originally identified as a human liver cDNA clone (Leytus, S.P., Loeb, K.R., Hagen, F.S., Kurachi, K., and Davie, E.W. (1988) Biochemistry 27, 1067-1074). In the present study the human hepsin gene was localized to chromosome 19 at q11-13.2. The messenger RNA of hepsin is 1.85 kilobases in size and present in most tissues, with the highest level in liver. Hepsin is synthesized as a single polypeptide chain, and its mature form of 51 kDa was found in various mammalian cells including HepG2 cells and baby hamster kidney cells. It is present in the plasma-membrane in a molecular orientation of type II membrane-associated proteins, with its catalytic subunit (carboxyl-terminal half) at the cell surface, and its amino terminus facing the cytosol. Hepsin is found neither in cytosol nor in culture media. The results obtained suggest that hepsin has an important role(s) in cell growth and function.

Amino Acid Sequence↗
PubMed1991

High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions.

Two symmetrical DNA-RNA-DNA duplex chimeras, d(CGCG)r(AAUU)d(CGCG) (designated rAAUU) and d(CGCG)r(UAUA)d(CGCG) (designated rUAUA), and a nonsymmetrical chimeric duplex, d(CGTT)r(AUAA)d(TGCG)/d(CGCA)r(UUAU)d(A ACG) (designated rAUAA), as well as their pure DNA analogues, containing dU instead of T, have been synthesized by solid-phase phosphoramidite methods and studied by high-resolution NMR techniques. The 1D imino proton NOE spectra of these d-r-d chimeras indicate normal Watson-Crick hydrogen bonding and base stacking at the junction region. Preliminary qualitative NOESY, COSY, and chemical shift data suggest that the internal RNA segment contains C3'-endo (A-type) sugar conformations except for the first RNA residues (position 5 and 17) following the 3' end of the DNA block, which, unlike the other six ribonucleotides, exhibit detectable H1'-H2' J coupling. The nucleosides of the two flanking DNA segments appear to adopt a fairly normal C2'-endo B-DNA conformation except at the junction with the RNA blocks (residues 4 and 16), where the last DNA residue appears to adopt an intermediate sugar conformation. The DNA-RNA junction residues exhibit quite different COSY, chemical shift, and NOE behavior, but these effects do not appear to propagate into the DNA or RNA segments. The circular dichroism spectra of these d-r-d chimeras also display a mixture of characteristic A-type and B-type absorption bands. The data indicate that A-type and B-type conformations can coexist in a single short continuous nucleic acid duplex, but our results differ somewhat from previous theoretical model studies.

Base Sequence↗
PubMed1991

Operative treatment of myasthenia gravis.

Although the relationship between the thymus gland and myasthenia gravis is still not clear, it has been recognized for many years that, however, early thymectomy can bring about remission or improvement of the disease. In the past 12 years, 40 myasthenic patients have received total thymectomies in the Department of Surgery, Kaohsiung Medical College Hospital. Their ages ranged from 13 to 68 years. They were classified according to Osserman's classification. After an average follow up period of 4 years, the total remission rate was 32.5%, and the improvement rate was 27.5%. The average interval between thymectomy and onset of remission was 12 months. The operative mortality was 5% and overall mortality 10%. Patients who received thymectomies under 40 years of age, short duration between disease onset and the thymectomy, milder preoperative symptoms and nontumorous thymuses, seemed to have better prognoses. Early thymectomy in childhood myasthenia gravis is still controversial. Although generally the ocular type was treated in a conservative manner, we had a 40% rate of surgical remission in this group. Total longitudinal median sternotomy is our choice of approach because the operative field is larger and the thymectomy is more complete. Thymectomy in immune diseases other than myasthenia gravis is one of our important points for future studies.

Adolescent↗
PubMed1991

Diaphragmatic injury.

From Feb. 1976 to Oct. 1990, 43 patients with diaphragmatic injuries were admitted to Kaohsiung Medical College Hospital. Blunt injuries occurred in 27 cases and penetrating injuries in 16 cases. The diagnosis is usually made by chest roentgenogram, chest CT, or during operations for other associated injuries. Delayed diagnoses were noted in 7 cases in blunt injury group and 2 cases in penetrating injury group. Isolated diaphragm injury was found in only 2 patients. The perforated diaphragm were almost repaired by two layers of continuous suture. None of them needed prosthetic mesh for reconstruction and no recurrence of hernia was found. In the blunt injury group, these patients usually combined with rib or long bone fractures, major intracranial injury, liver or spleen lacerations and intestinal perforations; while in the penetrating injury group, liver lacerations and stomach perforations were the most common associated injuries. Two deaths were noted in each group and the associated injury were accounted for these deaths.

Adolescent↗
PubMed1991

Characterization of hepsin, a membrane bound protease.

Hepsin is a membrane bound protease of 51 kDa present in mammalian cells. It contains a stretch of hydrophobic sequence of 27 amino acid residues in its N-terminal region. By employing fluorescent immunostaining of cells and western blot analysis of the various cell subfractions, the catalytic subunit (carboxyl terminal half) of hepsin is found at the cell surface. The hepsin gene is expressed in most tissues of a young adult baboon, particularly in the liver at high levels.

Animals↗
PubMed1991

Intrathoracic extramedullary hematopoiesis simulating posterior mediastinal mass--report of a case in patient with beta-thalassemia intermedia.

Intrathoracic involvement of the extramedullary hematopoiesis is a rare condition. It is usually found in patients with thalassemia or hereditary spherocytosis. In the literature, only 79 cases have been reported. Here, in Taiwan, a 22 year-old female patient of beta-thalassemia intermedia presented with posterior mediastinal mass proved as an intrathoracic extramedullary hematopoiesis by thoracoscopic biopsy was reported.

Adult↗
PubMed1989

Solid-phase synthesis and high-resolution NMR studies of two synthetic double-helical RNA dodecamers: r(CGCGAAUUCGCG) and r(CGCGUAUACGCG).

Ten-micromole solid-phase RNA synthesis has been successfully performed on an automated nucleic acid synthesizer with coupling efficiencies up to 99%, using the tert-butyldimethylsilyl group to protect the 2'-hydroxyl. The tert-butyldimethylsilyl group was easily removed by tetrabutylammonium fluoride under conditions in which virtually no 2'- to 3'-isomerization was found to occur. By use of this approach, the self-complementary RNA dodecamers r(CGCGAAUUCGCG) and r(CGCGUAUACGCG) were synthesized on an automated nucleic acid synthesizer, purified by TLC, and studied by high-resolution NMR. Imino protons were assigned from one-dimensional nuclear Overhauser effects. The nonexchangeable base, H1', and H2' protons were assigned by the sequential NOESY connectivity method. The NOE data from these two oligomers were analyzed qualitatively and compared to the ideal A- and B-type helix models of Arnott et al. (1972a,b). The internucleotide H6/H8 NOEs to the preceding H1' in r(CGCGUAUACGCG) were found to be sequence-dependent and probably reflect the roll angles between adjacent bases. The internucleotide H6/H8 to H2' NOEs of these oligomers correspond very well to an A-type conformation, but the interstrand adenine H2 NOEs to the following H1' were much stronger than those predicted from the fiber model. These srong interstrand NOEs can be rationalized by base pair slide to favor more interstrand base overlap, as predicted by Callidine and Drew (1984).

Base Composition↗
PubMed1989

High-resolution NMR study of a synthetic DNA-RNA hybrid dodecamer containing the consensus pribnow promoter sequence: d(CGTTATAATGCG).r(CGCAUUAUAACG).

The nonsymmetrical double-helical hybrid dodecamer d(CGTTATAATGCG).r(CGCAUUAUAACG) was synthesized with solid-phase phosphoramidite methods and studied by high-resolution 2D NMR. The imino protons were assigned by one-dimensional nuclear Overhauser methods. All the base protons and H1', H2', H2", H3', and H4' sugar protons of the DNA strand and the base protons, H1', H2', and most of the H3'-H4' protons of the RNA strand were assigned by 2D NMR techniques. The well-resolved spectra allowed a qualitative analysis of relative proton-proton distances in both strands of the dodecamer. The chemical shifts of the hybrid duplex were compared to those of the pure DNA double helix with the same sequence (Wemmer et al., 1984). The intrastrand and cross-strand NOEs from adenine H2 to H1' resonances of neighboring base pairs exhibited characteristic patterns that were very useful for checking the spectral assignments, and their highly nonsymmetric nature reveals that the conformations of the two strands are quite different. Detailed analysis of the NOESY and COSY spectra, as well as the chemical shift data, indicate that the RNA strand assumes a normal A-type conformation (C3'-endo) whereas the DNA strand is in the general S domain but not exactly in the normal C2'-endo conformation. The overall structure of this RNA-DNA duplex is different from that reported for hybrid duplexes in solution by other groups (Reid et al., 1983a; Gupta et al., 1985) and is closer to the C3'-endo-C2'-endo hybrid found in poly(dA).poly(dT) and poly(rU).poly(dA) in the fiber state (Arnott et al., 1983, 1986).

Computer Graphics↗
PubMed1988

Fibrin(ogen) peptide B beta 15-42 inhibits platelet aggregation and fibrinogen binding to activated platelets.

The binding of fibrinogen to activated platelets leads to platelet aggregation. Fibrinogen has multiple binding sites to platelet membrane glycoprotein IIb-IIIa complex. At least two well-defined sequences in fibrinogen, Arg-Gly-Asp sequence of A alpha 95-97 and A alpha 572-574 and gamma 400-411, have been shown to interact with glycoprotein IIb-IIIa. A possible binding site on the amino-terminal end of fibrinogen to platelet glycoprotein IIb-IIIa has also been reported. In this paper the effect of synthetic peptides derived from the amino-terminal end of the B beta chain on platelet aggregation and fibrinogen binding has been examined. B beta 15-42 peptide inhibits platelet aggregation and 125I-fibrinogen binding to activated platelets in a dose-dependent manner. Since B beta 15-42 contains a previously identified fibrinogen binding site, B beta 15-18, exposed by thrombin cleavage of native fibrinogen, we also examined the effect of B beta 15-18, B beta 19-42, and B beta 1-14 (fibrinopeptide B) on platelet aggregation and fibrinogen binding. Synthetic fibrinopeptide B and B beta 15-18 had no effect on platelet aggregation and fibrinogen binding while B beta 19-42 retained the inhibitory effect. When fibrinogen is chromatographed on a column of agarose-bound B beta 15-42, a cation-dependent retention of fibrinogen on the peptide column was observed, and fibrinogen was eluted from the column by B beta 15-42 but not by B beta 1-14. Under the same conditions, platelet glycoprotein IIb-IIIa was not retained in the column. Thus, the observed inhibitory effect is due to its interaction with fibrinogen rather than to platelet glycoprotein IIb-IIIa.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding Sites↗
PubMed1985

Duplex-hairpin transitions in DNA: NMR studies on CGCGTATACGCG.

Two dimensional NMR methods have been used to assign proton resonances in the high salt (greater than or equal to 100mM Na+), low temperature duplex form of the self-complementary DNA dodecamer d(CGCGTATACGCG). At low salt (less than or equal to 10mM Na+) and higher temperature marked changes in the two-dimensional spectrum, and in the one-dimensional spectrum reported by others, indicate that the molecule converts to an alternate conformation. Using saturation transfer methods, many of the resonances of this new conformation have been assigned, and the kinetics of the interconversion of the two forms has been studied. The linewidth, correlation time, and concentration dependence of the formation of this alternate conformation support the idea that it is a unimolecular hairpin. Observation of chemical shifts and NOEs in the hairpin conformation allow some preliminary structural characterization. Examination of the energetics of the interconversion suggests that the exchange between forms does not proceed through a single stranded intermediate, but rather through another pathway, probably involving a cruciform structure.

DNA↗
PubMed1984

Sequence-specific recognition of DNA. Nuclear magnetic resonance assignments and structural comparison of wild-type and mutant lambda OR3 operator DNA.

The resonances of all the base protons and most of the sugar protons in both strands of the 17 base-pair OR3 operator of the phage lambda, and of the vC3 single base-pair mutant, have been assigned using two-dimensional nuclear magnetic resonance methods. The chemical shift and nuclear Overhauser effect data for these two DNA sequences reveal no structural perturbation at sites distal to the mutation, neither are there significant changes in structure immediately surrounding the altered base-pair in the mutant sequence. These results are consistent with the model proposed by Ohlendorf et al. (1982), based on crystallographic data on the cro protein, for the OR3-cro protein interaction. The data from these solution studies are examined and discussed in the light of this model. This work demonstrates that nuclear magnetic resonance chemical shifts and nuclear Overhauser effect intensities provide a method for comparing the solution structures of DNA molecules. From the resolution available in the spectra of the 17 base-pair operators studied, it is clear that DNA duplexes of up to 30 or more base-pairs can be studied using phase-sensitive methods.

Bacteriophage lambda↗